SAN FRANCISCO —Colin Kaepernick kept running. He kept passing. He kept setting an example that many NFL teams envy and some NFL players can legitimately be afraid of.

This Saturday night in San Francisco belonged to the hometown 49ers, their second-year quarterback who’s on the verge of becoming a phenomenon, and the bold coach, Jim Harbaugh, who made a change that has changed his team — and could change the NFL and how players deal with injuries.

In Kaepernick’s first playoff start, he did everything right. He broke records, sped away with dazzling runs, completed hairpin passes.

“I don’t want to be categorized,” he said afterward, and indeed, it’s difficult to classify him as a better runner, passer or on-field leader.

The Washington Post’s LaVar Arrington, Dan Steinberg, Jason Reid and Jonathan Forsythe peer into their collective crystal balls to offer their bold predictions for the Redskins in 2013. (The Washington Post)

As he did it, Alex Smith stood on the sideline, where he’s been since Nov. 11. That’s when Smith, at the time the 49ers’ starter, suffered a concussion, giving way to Kaepernick, and eventually prompting Harbaugh to name the former Nevada star as his permanent starter.

When Harbaugh made that decision, it justified a fear that few NFL players talk about and gave life to a concern the NFL cannot afford. By getting injured and admitting it to his team’s training staff, Smith — the No. 1 overall draft pick in 2005 — lost his job and saw his future become murky. It became the perfect reason for a player to lie about an injury, regardless of the long-term health ramifications.

This is the same consideration that led Kansas City Chiefs quarterback Brady Quinn to conceal symptoms of a concussion earlier this season. At the time, Quinn said he was afraid that admitting his symptoms would land him back on the bench, where he’d been for three years. It’s the same worry that New York Jets quarterback Greg McElroy had when he “wasn’t exactly truthful,” as Coach Rex Ryan put it, about his own head injury. McElroy was the third quarterback who rose to become the starter, and suddenly an injury was going to derail his rise?

And it’s the same dangerous mentality that led Washington Redskins quarterback Robert Griffin III to continue playing last week against the Seattle Seahawks, despite a knee injury that not only rendered him mostly ineffective throughout most of that contest, but it also led to knee surgery on Wednesday and a long rehabilitation process that has his 2013 season in jeopardy.

“Mike [Shanahan] asked me if I was okay,” said Griffin, despite overwhelming evidence that he wasn’t himself. “I said yes.”

Griffin possessed job security that Quinn and McElroy lacked, as he is his team’s clear franchise quarterback. But this attitude isn’t about reality. It’s the motivational world that football players live in, the way they’re wired, and a belief that’s reinforced each day on NFL, college and even high-school practice fields: Play hard every day, show up, and know the difference between being hurt and being injured — or watch another player take your place.

Players throughout the NFL saw Smith benched two months ago because he admitted he was injured. They have since seen reasons, short-sighted as they are, for keeping quiet about injuries or playing them down to those paid to identify and treat them. Griffin avoided trainers and team doctors after spraining his LCL in early December, preventing senior orthopedic consultant James Andrews from examining him.

The league has worked for three years to take the taboo out of admitting a concussion or, for that matter, any injury. In a handful of weeks, that work has dissolved as Harbaugh made the football choice and went with Kaepernick as his starter. Smith was sidelined for a game and a half, and that was enough to change his season and career.

After Saturday’s win, Kaepernick stood in the locker room, smiling and posing for photographs. Smith stood mostly by himself at the adjoining locker, before grabbing his bag and heading, alone, toward the exit. While he walked, he was asked a question: If he could do it over, would he be honest? Or would he lie about his injury to remain the 49ers’ starter?

He chuckled before answering.

“Yeah, I’m not looking back,” he said, “worrying about anything that I do. Things happen. Obviously this is part of the deal. When you’re out, you give another guy an opportunity.”

Kaepernick was then ushered toward an interview room, where a team official held his bag as the quarterback first listened as teammates fawned over Kaepernick’s abilities; he then answered questions about how his night and season could’ve possibly gone better.

On Saturday, Kaepernick introduced himself again to America. He was better than the Packers’ Aaron Rodgers, the league’s most valuable player in 2011, and set the NFL record for most single-game rushing yards by a quarterback (181) and the franchise record for longest run (56 yards) by a quarterback. It also wasn’t so bad that he passed for 263 yards and two touchdowns, shaking off a pick-six on San Francisco’s first possession. Harbaugh told his quarterback that there was a lot of football left, and the young man took full advantage.

Kaepernick has abilities similar to Griffin’s, with a familiar brand of excitement, misdirection and unusual formations. He faked a handoff to running back Frank Gore in the third quarter Saturday, then ran to his right, past defenders, and all the way to the end zone.

“The end came down, our receivers blocked the corner and the safety,” Kaepernick said, “and there was nobody else left.”

On the 49ers’ next possession, he hit tight end Vernon Davis in stride on a 44-yard pass. The Packers had no idea which way to run, which play might be coming, how Kaepernick might beat them this time.

And it’s not as if Green Bay has an awful defense. The Packers were 11th in total defense throughout the regular season. Now they’re finished, the victims of another young quarterback who’s taking the NFL by storm.

The more Kaepernick wins, the easier it’ll be to forget about Smith in San Francisco, who still has two seasons remaining on his 49ers contract, though it would surprise no one if he’s traded during the offseason. But it’ll be difficult to forget how his time as the 49ers’ starter came to an end.

He was lost in the strong current of a young sensation, and that ride keeps going. With Kaepernick leading his team, most anything seems possible — and excitement, surprises and boldness seem guaranteed.

Saturday at Candlestick Park, he put on a show. It really was a heck of a thing to see — unless, of course, you’re the one standing on the sideline, watching the kid who took your job and wondering if being honest wasn’t the worst decision you could’ve made.

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